Negative stain particles how to prevent contrast invertion in 2D classification step?

[leetleyang]

From:

Easy template picking

Hi @ruiruigo, cryosparc is assuming you have cryo data and inverting the templates. Here’s a dark version of the template you can try (and then select “negative stain images” during particle extraction), however I found that cryosparc doesn’t work as well with the dark template and the options for data sign are confusing or buggy. What I do is to simply invert my micrographs before I import, and treat them like cryo data throughout the cryosparc processing. Here’s my full negative stain pipelin…

TL;DR, relevant line:

for i in *.mrc; do e2proc2d.py --mult=-1 $i ${i%.mrc}_inv.mrc; done